Clean up the code (0293ab53) · Commits · github_fork / Chromap

src/chromap.cc

+3 −18

Original line number	Diff line number	Diff line
		@@ -1146,8 +1146,6 @@ void Chromap<MappingRecord>::MapPairedEndReads() {
		negative_candidates2_buffer.clear();
		uint32_t repetitive_seed_length1 = 0;
		uint32_t repetitive_seed_length2 = 0;


		// Generate candidates
		if (mm_to_candidates_cache.Query(minimizers1, positive_candidates1, negative_candidates1, repetitive_seed_length1, read_batch1.GetSequenceLengthAt(pair_index)) == -1) {
		index.GenerateCandidates(error_threshold_, minimizers1, &repetitive_seed_length1, &positive_hits1, &negative_hits1, &positive_candidates1, &negative_candidates1);
		@@ -1339,18 +1337,6 @@ void Chromap<MappingRecord>::MapPairedEndReads() {

		mm_to_candidates_cache.Update(mm_history1[pair_index].minimizers, mm_history1[pair_index].positive_candidates, mm_history1[pair_index].negative_candidates, mm_history1[pair_index].repetitive_seed_length);
		mm_to_candidates_cache.Update(mm_history2[pair_index].minimizers, mm_history2[pair_index].positive_candidates, mm_history2[pair_index].negative_candidates, mm_history2[pair_index].repetitive_seed_length);
		/*if (mm_history1[pair_index].positive_candidates.size() < mm_history1[pair_index].positive_candidates.capacity() / 50) {
		std::vector<Candidate>().swap(mm_history1[pair_index].positive_candidates);
		}
		if (mm_history1[pair_index].negative_candidates.size() < mm_history1[pair_index].negative_candidates.capacity() / 50) {
		std::vector<Candidate>().swap(mm_history1[pair_index].negative_candidates);
		}
		if (mm_history2[pair_index].positive_candidates.size() < mm_history2[pair_index].positive_candidates.capacity() / 50) {
		std::vector<Candidate>().swap(mm_history2[pair_index].positive_candidates);
		}
		if (mm_history2[pair_index].negative_candidates.size() < mm_history2[pair_index].negative_candidates.capacity() / 50) {
		std::vector<Candidate>().swap(mm_history2[pair_index].negative_candidates);
		}*/

		if (mm_history1[pair_index].positive_candidates.size() > 50) {
		std::vector<Candidate>().swap(mm_history1[pair_index].positive_candidates);
		@@ -1408,7 +1394,6 @@ void Chromap<MappingRecord>::MapPairedEndReads() {
		std::cerr << "Mapped all reads in " << Chromap<>::GetRealTime() - real_start_mapping_time << "s.\n";
		delete[] mm_history1;
		delete[] mm_history2;
		//mm_to_candidates_cache.PrintStats();
		OutputMappingStatistics();
		if (!is_bulk_data_) {
		OutputBarcodeStatistics();

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